Fig. 5

Midpoint-rooted maximum likelihood phylogenetic tree of 1354 S. enterica genomes from the United States based on the alignment of 225,784 core SNPs. The scale bar represents the number of nucleotide substitutions per site. The black dots indicate the New Hampshire genomes. Full list of strain names, accession numbers and associated metadata can be found in Supplementary Table 6. The colors in the outer ring of the tree represent the 18 states from where the genomes came from, which also correspond to the colors on the map